how do people who have some automated process (like me with my Makefile)
to produce PKGBUILD and .SRCINFO typically deal with this, structure
things?  (i don't *think* i saw any mention of this in the various wiki
pages; apologies if i missed something.)

The general method is to keep the automation not in the repository (path) where the PKGBUILD and .SRCINFO reside. aurpublish[1] for example helps you set up a single source repository. Any packaging utilities can live in the repository root while subfolders contain the PKGBUILDs.

[1]: https://archlinux.org/packages/community/any/aurpublish/

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